GROMACS Initial Setup Error

usegalaxy.eu support
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Hello,

I am currently trying out the “Hands on: High Throughput Molecular Dynamics and Analysis” tutorial with other data and ran into a problem with the ‘GROMACS Initial Setup” tool. Despite having no errors with the separation of the HETATMs from the protein, the tool failed to generate the TOP, GRO, or ITP files from the PDB file. I tried using the usegalaxy.org server, but I ran into the same problem. I suspect it was because of the PDB file having missing records, but I am not knowledgeable enough about that topic to confirm if that was the case. I have provided my history here.

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Welcome @i3l_ezekielmeliala

We have been very busy! If you solved this already, please let us know. And if not, maybe I can provide a few clues about where to find the jobs logs for this tool! These will be the same logs as one would get when running the tool directly – so these are really important! Especially when processing a new pdb dataset that may need some extra manipulations to have it work well in a simlulation!

This first screenshot is from your error. Checking the box to output the detailed log was a good choice! There is a message here that is referring to the content of the parsed protein file. Note: most tools do not have a separate log output in the history – find the job logs from the tool using the Details i-icon instead (where all inputs and outputs are summarized, all tools, any job) – and you can see that view in the tabs too!

gromacs-1-log
gromacs-1-log1920×1465 510 KB

Then, just to get an idea about what those lines are the input file, next, try to review the data if it is available in plain text. After that, you can try to parse the file with text manipulation tools to investigate. Then use that information to review the documentation and help for the underlying tool.

gromacs-2-data-to-review
gromacs-2-data-to-review1920×1472 512 KB

Gromacs, and most tools, will work the same in Galaxy as they do in other places. This means you can search error messages, review tutorials, visit scientific forums, and even ask AI chat bots! They tend to be really great at summarizing complex scientific tool manual documentation. I personally wouldn’t let an AI analyze my data but they certainly can help when learning how to use a tool.

Whenever you are not sure if the message from a tool is from the underlying tool or Galaxy itself (the clusters running the tool), please come back here and we can help to sort out what is going on.

What to do

Your current error is related to the data content and what Gromacs is expecting to process. It seems you will need to pre-process your pdb dataset a bit more since simply filtering for protein atoms was not enough. The underlying data is missing at least one side chain. So, you guess was spot on!

You can try a tool like this one in Galaxy to see if it is enough.

  • PDBFixer to automatically fix a PDB file before performing molecular dynamics simulation

Hopefully this helps you to get oriented! :slight_smile: